Covalent organic frameworks (COFs) have been studied with density functional theory (DFT) calculations. We investigated the stacking preference for the COF-1, -5, -6 and -10 by comparing the features of the optimized structures of possible arrangement. After the validation of the suitable functional, staggered and eclipsed stacking structures were modeled based on the experimental data, and were compared in terms of relative energy. In the case of staggered stacking of COF-1, the interaction between B and O atom is possible, and the π–π stacking of aromatic rings is observed for the eclipsed arrangement of both COF-1 and -6. Electrostatic interaction in the staggered form of COF-1 makes the charge separation between the boron atom and oxygen atom in the neighboring layers supported by the partial density of states (PDOS) analysis.